I believe that it will always show the message count no matter what you do. The crazy thing is that you really cannot shut the messaging program off. You are just shutting down the notifications. It would be nice to be able to turn the SMS/MMS part of it off and just leave the voicemail stuff on.
Basically you may use more battery up using Handcent since the messaging app and Handcent are doing double duty.
Using Handcent doesn't use any more battery than using the stock app.
I think he just needs to remove the messaging icon from the home screen. If you're not using it and Handcent is set as your default just swap icons and turn off notification on the stock app.